1,965 results match your criteria Algebra Universalis[Journal]


Biomarkers of pre-existing risk of Torsade de Pointes under Sotalol treatment.

J Electrocardiol 2020 May 4;60:177-183. Epub 2020 May 4.

Instituto de Ingeniería Biomédica, UBA, Paseo Colón 850 (C1063ACV), Buenos Aires, Argentina; Instituto Argentino de Matemática 'Alberto P. Calderón', CONICET, Saavedra 15 (C1083ACA), Buenos Aires, Argentina.

Introduction: Antiarrhythmic drugs therapies are currently going through a turning point. The high risk that exists during the treatments has led to an ongoing search for new non-invasive toxicity risk biomarkers.

Methods: We propose the use of spatial biomarkers obtained through the quaternion algebra, evaluating the dynamics of the cardiac electrical vector in a non-invasive way in order to detect abnormal changes in ventricular heterogeneity. Read More

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http://dx.doi.org/10.1016/j.jelectrocard.2020.04.011DOI Listing

Onsager's Scars in Disordered Spin Chains.

Phys Rev Lett 2020 May;124(18):180604

Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan.

We propose a class of nonintegrable quantum spin chains that exhibit quantum many-body scars even in the presence of disorder. With the use of the so-called Onsager symmetry, we construct scarred models for arbitrary spin quantum number S. There are two types of scar states, namely, coherent states associated with an Onsager-algebra element and one-magnon scar states. Read More

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http://dx.doi.org/10.1103/PhysRevLett.124.180604DOI Listing

Vulnerability to severe forms of COVID-19: an intra-municipal analysis in the city of Rio de Janeiro, Brazil.

Cad Saude Publica 2020;36(5):e00075720. Epub 2020 May 18.

Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.

Given the characteristics of the COVID-19 pandemic and the limited tools for orienting interventions in surveillance, control, and clinical care, the current article aims to identify areas with greater vulnerability to severe cases of the disease in Rio de Janeiro, Brazil, a city characterized by huge social and spatial heterogeneity. In order to identify these areas, the authors prepared an index of vulnerability to severe cases of COVID-19 based on the construction, weighting, and integration of three levels of information: mean number of residents per household and density of persons 60 years or older (both per census tract) and neighborhood tuberculosis incidence rate in the year 2018. The data on residents per household and density of persons 60 years or older were obtained from the 2010 Population Census, and data on tuberculosis incidence were taken from the Brazilian Information System for Notificable Diseases (SINAN). Read More

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http://dx.doi.org/10.1590/0102-311x00075720DOI Listing

Semiautomatic construction of lattice Boltzmann models.

Phys Rev E 2020 Apr;101(4-1):043310

Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany and Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia.

A crucial step in constructing a lattice Boltzmann model is the definition of a suitable set of lattice velocities and the correct assignment of the associated weights. For high-order models, the solution of this problem requires a nontrivial effort. This paper outlines the functioning of a publicly available Python script which has been written to assist researchers in that task. Read More

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http://dx.doi.org/10.1103/PhysRevE.101.043310DOI Listing

ReSpect: Relativistic spectroscopy DFT program package.

J Chem Phys 2020 May;152(18):184101

Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, SK-84536 Bratislava, Slovakia.

With the increasing interest in compounds containing heavier elements, the experimental and theoretical community requires computationally efficient approaches capable of simultaneous non-perturbative treatment of relativistic, spin-polarization, and electron correlation effects. The ReSpect program has been designed with this goal in mind and developed to perform relativistic density functional theory (DFT) calculations on molecules and solids at the quasirelativistic two-component (X2C Hamiltonian) and fully relativistic four-component (Dirac-Coulomb Hamiltonian) level of theory, including the effects of spin polarization in open-shell systems at the Kramers-unrestricted self-consistent field level. Through efficient algorithms exploiting time-reversal symmetry, biquaternion algebra, and the locality of atom-centered Gaussian-type orbitals, a significant reduction of the methodological complexity and computational cost has been achieved. Read More

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http://dx.doi.org/10.1063/5.0005094DOI Listing

Time series modelling to forecast the confirmed and recovered cases of COVID-19.

Travel Med Infect Dis 2020 May 13:101742. Epub 2020 May 13.

Fractional Calculus, Optimization and Algebra Research Group, Faculty of Mathematics and Statistics, Ton Duc Thang University, Ho Chi Minh City, Vietnam. Electronic address:

Coronaviruses are enveloped RNA viruses from the Coronaviridae family affecting neurological, gastrointestinal, hepatic and respiratory systems. In late 2019 a new member of this family belonging to the Betacoronavirus genera (referred to as COVID-19) originated and spread quickly across the world calling for strict containment plans and policies. In most countries in the world, the outbreak of the disease has been serious and the number of confirmed COVID-19 cases has increased daily, while, fortunately the recovered COVID-19 cases have also increased. Read More

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http://dx.doi.org/10.1016/j.tmaid.2020.101742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219401PMC

Performance data of multiple-precision scalar and vector BLAS operations on CPU and GPU.

Data Brief 2020 Jun 21;30:105506. Epub 2020 Apr 21.

Department of Electronic Computing Machines, Vyatka State University, Russian Federation.

Many optimized linear algebra packages support the single- and double-precision floating-point data types. However, there are a number of important applications that require a higher level of precision, up to hundreds or even thousands of digits. This article presents performance data of four dense basic linear algebra subprograms - ASUM, DOT, SCAL, and AXPY - implemented using existing extended-/multiple-precision software for conventional central processing units and CUDA compatible graphics processing units. Read More

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http://dx.doi.org/10.1016/j.dib.2020.105506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195515PMC

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.

Brief Bioinform 2020 May 4. Epub 2020 May 4.

Monash Biomedicine Discovery Institute, Monash University, Australia. He is also affiliated with the Monash Centre for Data Science, Faculty of Information Technology, Monash University. His research interests include bioinformatics, computational biology, machine learning, data mining, and pattern recognition.

Promoters are short consensus sequences of DNA, which are responsible for transcription activation or the repression of all genes. There are many types of promoters in bacteria with important roles in initiating gene transcription. Therefore, solving promoter-identification problems has important implications for improving the understanding of their functions. Read More

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http://dx.doi.org/10.1093/bib/bbaa049DOI Listing

Wedge reversion antisymmetry and 41 types of physical quantities in arbitrary dimensions.

Acta Crystallogr A Found Adv 2020 May 28;76(Pt 3):318-327. Epub 2020 Apr 28.

Department of Materials Science and Engineering, Department of Physics, and Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.

It is shown that there are 41 types of multivectors representing physical quantities in non-relativistic physics in arbitrary dimensions within the formalism of Clifford algebra. The classification is based on the action of three symmetry operations on a general multivector: spatial inversion, 1, time-reversal, 1', and a third that is introduced here, namely wedge reversion, 1. It is shown that the traits of `axiality' and `chirality' are not good bases for extending the classification of multivectors into arbitrary dimensions, and that introducing 1 would allow for such a classification. Read More

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http://dx.doi.org/10.1107/S205327332000217XDOI Listing

Three types of logical structure resulting from the trilemma of free will, determinism and locality.

Biosystems 2020 Apr 28;195:104151. Epub 2020 Apr 28.

Centre for Unconventional Computing, University of West England, Coldharbour Ln., Stoke Gilfford, Bristol, BS16 QY, United Kingdom.

How can one defend free will against determinism? Since quantum mechanics entails non-locality, it enables the co-existence of free will and determinism. Is non-locality in cognition possible, or must quantum mechanics be rejected? Here, we define free will, determinism and locality in terms of a binary relation between objects and representations, and we verify that the three concepts constitute a trilemma. We also show that non-locality in cognition is naturally found in decision making without any assumption of quantum mechanics. Read More

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http://dx.doi.org/10.1016/j.biosystems.2020.104151DOI Listing

An Item Response Model for True-False Exams Based on Signal Detection Theory.

Appl Psychol Meas 2020 May 23;44(3):234-248. Epub 2019 Apr 23.

Columbia University, New York, NY, USA.

A true-false exam can be viewed as being a signal detection task-the task is to detect whether or not an item is true (signal) or false (noise). In terms of signal detection theory (SDT), examinees can be viewed as performing the task by comparing the perceived plausibility of an item (a perceptual component) to a threshold that delineates true from false (a decision component). The resulting model is distinct yet is related to item response theory (IRT) models and grade of membership models, with the difference that SDT explicitly recognizes the role of examinees' perceptions in determining their response to an item. Read More

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http://dx.doi.org/10.1177/0146621619843823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7174808PMC

Mapping functional brain networks from the structural connectome: Relating the series expansion and eigenmode approaches.

Neuroimage 2020 Apr 23;216:116805. Epub 2020 Apr 23.

Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Clinical Neurophysiology and MEG Center, Amsterdam Neuroscience, Amsterdam, the Netherlands.

Functional brain networks are shaped and constrained by the underlying structural network. However, functional networks are not merely a one-to-one reflection of the structural network. Several theories have been put forward to understand the relationship between structural and functional networks. Read More

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http://dx.doi.org/10.1016/j.neuroimage.2020.116805DOI Listing

Effect of Reconstruction Algorithm on the Identification of 3D Printing Polymers Based on Hyperspectral CT Technology Combined with Artificial Neural Network.

Materials (Basel) 2020 Apr 22;13(8). Epub 2020 Apr 22.

Instrument and Electrical Department, School of Aerospace Engineering, Xiamen University, Xiamen 361102, China.

Hyperspectral X-ray CT (HXCT) technology provides not only structural imaging but also the information of material components therein. The main purpose of this study is to investigate the effect of various reconstruction algorithms on reconstructed X-ray absorption spectra (XAS) of components shown in the CT image by means of HXCT. In this paper, taking 3D printing polymer as an example, seven kinds of commonly used polymers such as thermoplastic elastomer (TPE), carbon fiber reinforced polyamide (PA-CF), acrylonitrile butadiene styrene (ABS), polylactic acid (PLA), ultraviolet photosensitive resin (UV9400), polyethylene terephthalate glycol (PETG), and polyvinyl alcohol (PVA) were selected as samples for hyperspectral CT reconstruction experiments. Read More

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http://dx.doi.org/10.3390/ma13081963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7216274PMC

Spatial-temporal variability of rainfall and mean air temperature for the state of Bahia, Brazil.

An Acad Bras Cienc 2020 22;92(1):e20181283. Epub 2020 Apr 22.

Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Rod. Jorge Amado, Km 16, Salobrinho, 45662-900 Ilhéus, BA, Brazil.

The aim of this study was to evaluate spatial behavior and temporal stability of rainfall and mean air temperature in the state of Bahia, using historical series from 1975 to 2011 and 1961 to 2009, respectively. The analyses were performed considering the accumulated variables of each month of the historical series. The accumulated monthly totals were divided by the number of years of observation, obtaining the monthly average values ​​of rainfall and air temperature for each measurement point. Read More

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http://dx.doi.org/10.1590/0001-3765202020181283DOI Listing

Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin.

Dev Biol 2020 Apr 19. Epub 2020 Apr 19.

Departments of Genetics and Development, and Dermatology, Columbia University Medical Center, New York, NY, 10032, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA. Electronic address:

Animal development and homeostasis depend on precise temporal and spatial intercellular signaling. Components shared between signaling pathways, generally thought to decrease specificity, paradoxically can also provide a solution to pathway coordination. Here we show that the Bone Morphogenetic Protein (BMP) and Wnt signaling pathways share Apcdd1 as a common inhibitor and that Apcdd1 is a taxon-restricted gene with novel domains and signaling functions. Read More

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http://dx.doi.org/10.1016/j.ydbio.2020.03.015DOI Listing

Social determinants of colorectal cancer risk, stage, and survival: a systematic review.

Int J Colorectal Dis 2020 Jun 21;35(6):985-995. Epub 2020 Apr 21.

Department of Population Health Sciences, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 3091, USA.

Background: Several social determinants of health have been examined in relation to colorectal cancer incidence, stage at diagnosis, and survival including income, education, neighborhood disadvantage, immigration status, social support, and social network. Colorectal cancer incidence rates are positively associated with income and other measures of socioeconomic status. In contrast, low socioeconomic status tends to be associated with poorer survival. Read More

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http://dx.doi.org/10.1007/s00384-020-03585-zDOI Listing

Epigenetic pacemaker: closed form algebraic solutions.

Authors:
Sagi Snir

BMC Genomics 2020 Apr 16;21(Suppl 2):257. Epub 2020 Apr 16.

Department of Evolutionary & Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel.

Background: DNA methylation is widely used as a biomarker in crucial medical applications as well as for human age prediction of very high accuracy. This biomarker is based on the methylation status of several hundred CpG sites. In a recent line of publications we have adapted a versatile concept from evolutionary biology - the Universal Pacemaker (UPM) - to the setting of epigenetic aging and denoted it the Epigenetic PaceMaker (EPM). Read More

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http://dx.doi.org/10.1186/s12864-020-6606-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161103PMC

New Global Referencing Approach in a Camera-LCD Micro Positioning System.

Sensors (Basel) 2020 Apr 9;20(7). Epub 2020 Apr 9.

Department of Geometry and Topology, University of Granada, 18071 Granada, Spain.

In any precision manufacturing process, positioning systems play a very important role in achieving a quality product. As a new approach to current systems, camera-LCD positioning systems are a new technology that can provide substantial improvements enabling better accuracy and repeatability. However, in order to provide stability to the system a global positioning system is required. Read More

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http://dx.doi.org/10.3390/s20072118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7181139PMC

Galois Conjugated Tensor Fusion Categories and Nonunitary Conformal Field Theory.

Phys Rev Lett 2020 Mar;124(12):120601

Department of Physics and Astronomy, Ghent University, Krijgslaan 281, S9, B-9000 Ghent, Belgium.

We provide a generalization of the matrix product operator formalism for string-net projected entangled pair states (PEPS) to include nonunitary solutions of the pentagon equation. These states provide the explicit lattice realization of the Galois conjugated counterparts of (2+1)-dimensional topological quantum field theories, based on tensor fusion categories. Although the parent Hamiltonians of these renormalization group fixed point states are gapless, these states can still be the topological ground states of a gapped non-Hermitian Hamiltonian. Read More

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http://dx.doi.org/10.1103/PhysRevLett.124.120601DOI Listing

A Visual Attentive Model for Discovering Patterns in Eye-Tracking Data-A Proposal in Cultural Heritage.

Sensors (Basel) 2020 Apr 8;20(7). Epub 2020 Apr 8.

Dipartimento di Ingegneria dell'Informazione, Universitá Politecnica delle Marche, 60131 Ancona, Italy.

In the Cultural Heritage (CH) context, art galleries and museums employ technology devices to enhance and personalise the museum visit experience. However, the most challenging aspect is to determine what the visitor is interested in. In this work, a novel Visual Attentive Model (VAM) has been proposed that is learned from eye tracking data. Read More

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http://dx.doi.org/10.3390/s20072101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180873PMC

MetaChem: An Algebraic Framework for Artificial Chemistries.

Artif Life 2020 Apr 9:153-195. Epub 2020 Apr 9.

University of York, Department of Computer Science, York Cross-disciplinary Centre for Systems Analysis.

We introduce MetaChem, a language for representing and implementing artificial chemistries. We motivate the need for modularization and standardization in representation of artificial chemistries. We describe a mathematical formalism for Static Graph MetaChem, a static-graph-based system. Read More

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http://dx.doi.org/10.1162/artl_a_00315DOI Listing

Gait Rhythm Dynamics for Neuro-Degenerative Disease Classification via Persistence Landscape- Based Topological Representation.

Sensors (Basel) 2020 Apr 3;20(7). Epub 2020 Apr 3.

Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, No. 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen 518055, China.

Neuro-degenerative disease is a common progressive nervous system disorder that leads to serious clinical consequences. Gait rhythm dynamics analysis is essential for evaluating clinical states and improving quality of life for neuro-degenerative patients. The magnitude of stride-to-stride fluctuations and corresponding changes over time-gait dynamics-reflects the physiology of gait, in quantifying the pathologic alterations in the locomotor control system of health subjects and patients with neuro-degenerative diseases. Read More

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http://dx.doi.org/10.3390/s20072006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180793PMC
April 2020
2.245 Impact Factor

Radical factorization in finitary ideal systems.

Commun Algebra 2020 26;48(1):228-253. Epub 2019 Jul 26.

Department of Mathematical Sciences, New Mexico State University, Las Cruces, NM, USA.

In this article, we investigate the concept of radical factorization with respect to finitary ideal systems of cancellative monoids. We present new characterizations for -almost Dedekind -SP-monoids and provide specific descriptions of -almost Dedekind -SP-monoids and -SP-monoids. We show that a monoid is a -SP-monoid if and only if the radical of every nontrivial principal ideal is -invertible. Read More

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http://dx.doi.org/10.1080/00927872.2019.1640237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077461PMC

Classification of Rota-Baxter operators on semigroup algebras of order two and three.

Commun Algebra 2019 4;47(8):3094-3116. Epub 2019 Mar 4.

Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria.

In this paper, we determine all the Rota-Baxter operators of weight zero on semigroup algebras of order two and three with the help of computer algebra. We determine the matrices for these Rota-Baxter operators by directly solving the defining equations of the operators. We also produce a Mathematica procedure to predict and verify these solutions. Read More

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http://dx.doi.org/10.1080/00927872.2018.1552278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083595PMC

Linear algebraic structure of zero-determinant strategies in repeated games.

PLoS One 2020 2;15(4):e0230973. Epub 2020 Apr 2.

Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Japan.

Zero-determinant (ZD) strategies, a recently found novel class of strategies in repeated games, has attracted much attention in evolutionary game theory. A ZD strategy unilaterally enforces a linear relation between average payoffs of players. Although existence and evolutional stability of ZD strategies have been studied in simple games, their mathematical properties have not been well-known yet. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0230973PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117786PMC

Resolution of 4 components in the same pixel in FLIM images using the phasor approach.

Methods Appl Fluoresc 2020 Apr 15;8(3):035001. Epub 2020 Apr 15.

Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, United States of America.

In several cellular systems, the phasor FLIM approach has shown the existence of more than 2 components in the same pixel, a typical example being free and bound NADH. In order to properly quantify the concentrations and the spatial distributions of fluorescence components associated with different molecular species we developed a general method to resolve 3 and 4 components in the same pixel using the phasor approach. The method is based on the law of linear combination of components valid after transformation of the decay curves to phasors for each pixel in the image. Read More

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http://dx.doi.org/10.1088/2050-6120/ab8570DOI Listing

Discrete-time population dynamics on the state space of measures.

Authors:
Horst R Thieme

Math Biosci Eng 2019 11;17(2):1168-1217

School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85287-1804, USA.

If the individual state space of a structured population is given by a metric space , measures on the -algebra of Borel subsets of offer a modeling tool with a natural interpretation: () is the number of individuals with structural characteristics in the set . A discrete-time population model is given by a on the cone of finite nonnegative Borel measures that maps the structural population distribution of a given year to the one of the next year. Under suitable assumptions, has a first order approximation at the zero measure (the extinction fixed point), which is a positive linear operator on the ordered vector space of real measures and can be interpreted as a . Read More

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http://dx.doi.org/10.3934/mbe.2020061DOI Listing
November 2019

Variational Density Fitting with a Krylov Subspace Method.

J Chem Theory Comput 2020 May 20;16(5):2965-2974. Epub 2020 Apr 20.

Programa de Doctorado de Nanociencias y Nanotecnologı́as, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico.

In this work, we present the implementation of a variational density fitting methodology that uses iterative linear algebra for solving the associated system of linear equations. It is well known that most difficulties with this system arise from the fact that the coefficient matrix is in general ill-conditioned and, due to finite precision round-off errors, it may not be positive definite. The dimensionality, given by the number of auxiliary functions, also poses a challenge in terms of memory and time demand since the coefficient matrix is dense. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b01212DOI Listing

On the Parity Under Metapletic Operators and an Extension of a Result of Lyubarskii and Nes.

Authors:
Markus Faulhuber

Results Math 2020 5;75(1). Epub 2019 Dec 5.

NuHAG, Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria.

In this work we show that if the frame property of a Gabor frame with window in Feichtinger's algebra and a fixed lattice only depends on the parity of the window, then the lattice can be replaced by any other lattice of the same density without losing the frame property. As a byproduct we derive a generalization of a result of Lyubarskii and Nes, who could show that any Gabor system consisting of an odd window function from Feichtinger's algebra and any separable lattice of density , , cannot be a Gabor frame for the Hilbert space of square-integrable functions on the real line. We extend this result by removing the assumption that the lattice has to be separable. Read More

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http://dx.doi.org/10.1007/s00025-019-1134-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7072060PMC
December 2019

The cluster randomized crossover trial: The effects of attrition in the AB/BA design and how to account for it in sample size calculations.

Authors:
Mirjam Moerbeek

Clin Trials 2020 Mar 19:1740774520913042. Epub 2020 Mar 19.

Department of Methodology and Statistics, Utrecht University, Utrecht, The Netherlands.

Background/aims: This article studies the effect of attrition in the cluster randomized crossover trial. The focus is on the two-treatment two-period AB/BA design where attrition occurs during the washout period. Attrition may occur at either the subject level or the cluster level. Read More

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http://dx.doi.org/10.1177/1740774520913042DOI Listing

Response to: Simpson's Paradox is suppression, but Lord's Paradox is neither: clarification of and correction to Tu, Gunnell, and Gilthorpe (2008) by Nickerson CA & Brown NJL (https://doi.org/10.1186/1742-7622-5-2).

Emerg Themes Epidemiol 2020 11;17. Epub 2020 Mar 11.

4Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.

We commend Nickerson and Brown on their insightful exposition of the mathematical algebra behind Simpson's paradox, suppression and Lord's paradox; we also acknowledge there can be differences in how Lord's paradox is approached analytically, compared to Simpson's paradox and suppression, though not in every example of Lord's paradox. Furthermore, Simpson's paradox, suppression and Lord's paradox ask the same questions, seeking to understand if statistical adjustment is valid and meaningful, identifying which analytical option is correct. In our exposition of this, we focus on the perspective of context, which must invoke causal thinking. Read More

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http://dx.doi.org/10.1186/s12982-020-00089-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7066787PMC

Projected t-SNE for batch correction.

Bioinformatics 2020 Mar 16. Epub 2020 Mar 16.

Department of Statistical Science, Duke University, Durham, NC, USA.

Motivation: Low-dimensional representations of high-dimensional data are routinely employed in biomedical research to visualize, interpret and communicate results from different pipelines. In this article, we propose a novel procedure to directly estimate t-SNE embeddings that are not driven by batch effects. Without correction, interesting structure in the data can be obscured by batch effects. Read More

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http://dx.doi.org/10.1093/bioinformatics/btaa189DOI Listing

BLAMM: BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs.

Authors:
Jan Fostier

BMC Bioinformatics 2020 Mar 11;21(Suppl 2):81. Epub 2020 Mar 11.

Department of Information Technology - IDLab, Ghent University - imec, Technologiepark 126, Ghent (Zwijnaarde), B-9052, Belgium.

Background: The identification of all matches of a large set of position weight matrices (PWMs) in long DNA sequences requires significant computational resources for which a number of efficient yet complex algorithms have been proposed.

Results: We propose BLAMM, a simple and efficient tool inspired by high performance computing techniques. The workload is expressed in terms of matrix-matrix products that are evaluated with high efficiency using optimized BLAS library implementations. Read More

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http://dx.doi.org/10.1186/s12859-020-3348-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068855PMC

Conditions of experienced stigma in people living with HIV in Iran: a qualitative comparative analysis.

Sociol Health Illn 2020 Mar 11. Epub 2020 Mar 11.

Department of Sociology, Tarbiat Modares University, Tehran, Iran.

Stigma against people living with HIV (PLWH) seriously affects their quality of life. Moreover it can lead them to hide their HIV status from others, which in turn endangers public health. Many studies dealing with HIV-related stigma focus on the consequences of this phenomenon and pay less attention to the social conditions which affect different types of HIV-related stigma (anticipated, internalized and enacted stigma [ES]). Read More

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http://dx.doi.org/10.1111/1467-9566.13077DOI Listing

The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.

PLoS Comput Biol 2020 Mar 9;16(3):e1007651. Epub 2020 Mar 9.

Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom.

Biological systems are made up of components that change their actions (and interactions) over time and coordinate with other components nearby. Together with a large state space, the complexity of this behaviour can make it difficult to create concise mathematical models that can be easily extended or modified. This paper introduces the Beacon Calculus, a process algebra designed to simplify the task of modelling interacting biological components. Read More

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http://dx.doi.org/10.1371/journal.pcbi.1007651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082070PMC

The 'algebra of evolution': the Robertson-Price identity and viability selection for body mass in a wild bird population.

Philos Trans R Soc Lond B Biol Sci 2020 Apr 9;375(1797):20190359. Epub 2020 Mar 9.

Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.

By the Robertson-Price identity, the change in a quantitative trait owing to selection, is equal to the trait's covariance with relative fitness. In this study, we applied the identity to long-term data on superb fairy-wrens , to estimate phenotypic and genetic change owing to juvenile viability selection. Mortality in the four-week period between fledging and independence was 40%, and heavier nestlings were more likely to survive, but why? There was additive genetic variance for both nestling mass and survival, and a positive phenotypic covariance between the traits, but no evidence of additive genetic covariance. Read More

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http://dx.doi.org/10.1098/rstb.2019.0359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133512PMC

Joining and decomposing reaction networks.

J Math Biol 2020 May 2;80(6):1683-1731. Epub 2020 Mar 2.

Texas A&M University, College Station, USA.

In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-level behavior. However, the theory for tackling these larger systems in general has lagged behind. Here, we analyze how joining networks (e. Read More

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http://dx.doi.org/10.1007/s00285-020-01477-yDOI Listing

Landmarks of the Knowledge and Biology in the Wild Environment.

Front Cell Infect Microbiol 2020 6;10:10. Epub 2020 Feb 6.

Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.

Trypanosomatids are ancient parasitic eukaryotes that still maintain prokaryotic characteristics. , a primarily wild mammal parasite, infected humans already long before European colonization of the Americas. heterogeneity remains an unsolved question, and until now, it has still not been possible to associate genotypes with any biological or epidemiological feature. Read More

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http://dx.doi.org/10.3389/fcimb.2020.00010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016096PMC
February 2020

SquidLab-A user-friendly program for background subtraction and fitting of magnetization data.

Rev Sci Instrum 2020 Feb;91(2):023901

Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.

We present an open-source program free to download for academic use with a full user-friendly graphical interface for performing flexible and robust background subtraction and dipole fitting on magnetization data. For magnetic samples with small moment sizes or sample environments with large or asymmetric magnetic backgrounds, it can become necessary to separate background and sample contributions to each measured raw voltage measurement before fitting the dipole signal to extract magnetic moments. Originally designed for use with pressure cells on a Quantum Design MPMS3 SQUID magnetometer, SquidLab is a modular object-oriented platform implemented in Matlab with a range of importers for different widely available magnetometer systems (including MPMS, MPMS-XL, MPMS-IQuantum, MPMS3, and S700X models) and has been tested with a broad variety of background and signal types. Read More

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http://dx.doi.org/10.1063/1.5137820DOI Listing
February 2020

Parametric controllability of the personalized PageRank: Classic model vs biplex approach.

Chaos 2020 Feb;30(2):023115

Department of Applied Mathematics, Rey Juan Carlos University, 28933 Madrid, Spain.

Measures of centrality in networks defined by means of matrix algebra, like PageRank-type centralities, have been used for over 70 years. Recently, new extensions of PageRank have been formulated and may include a personalization (or teleportation) vector. It is accepted that one of the key issues for any centrality measure formulation is to what extent someone can control its variability. Read More

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http://dx.doi.org/10.1063/1.5128567DOI Listing
February 2020

PyBERTHART: A Relativistic Real-Time Four-Component TDDFT Implementation Using Prototyping Techniques Based on Python.

J Chem Theory Comput 2020 Apr 9;16(4):2410-2429. Epub 2020 Mar 9.

Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy.

We present a real-time time-dependent four-component Dirac-Kohn-Sham (RT-TDDKS) implementation based on the BERTHA code. This new implementation takes advantage of modern software engineering, including the prototyping techniques. The software design follows a three step approach: (i) the prototype implementation of a time-propagation algorithm in nonrelativistic real-time TDDFT within the Psi4NumPy framework, which provides a suitable environment for the creation of a clear, readable, and easy to test reference code in Python, (ii) the design of an original Python application programming interface for the relativistic four-component code BERTHA (PyBERTHA), which has an efficient computational kernel for relativistic integrals written in FORTRAN, and (iii) the porting of the time-propagation scheme enveloped within the Psi4NumPy framework to PyBERTHA. Read More

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http://dx.doi.org/10.1021/acs.jctc.0c00053DOI Listing

Homology-based radiomic features for prediction of the prognosis of lung cancer based on CT-based radiomics.

Med Phys 2020 Jun 16;47(5):2197-2205. Epub 2020 Mar 16.

Department of Radiation Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan.

Purpose: Radiomics is a new technique that enables noninvasive prognostic prediction by extracting features from medical images. Homology is a concept used in many branches of algebra and topology that can quantify the contact degree. In the present study, we developed homology-based radiomic features to predict the prognosis of non-small-cell lung cancer (NSCLC) patients and then evaluated the accuracy of this prediction method. Read More

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http://dx.doi.org/10.1002/mp.14104DOI Listing

Customized FreeSurfer-based brain atlas for diffeomorphic anatomical registration through exponentiated lie algebra tool.

Ann Nucl Med 2020 Apr 22;34(4):280-288. Epub 2020 Feb 22.

Department of Neurology, Gangnam Severance Hospital, Yonsei University College of Medicine, 20 Eonjuro 63-gil, Gangnam-gu, Seoul, Republic of Korea.

Objective: Digital brain template and atlas designed for a specific group provide advantages for the analysis and interpretation of neuroimaging data, but require a significant workload for development. We developed a simple method to create customized brain atlas for diffeomorphic anatomical registration through exponentiated lie algebra (DARTEL) tool using FreeSurfer-generated volume-of-interest (FSVOI) images and validated.

Methods: F-florbetaben positron emission tomography (PET) and magnetic resonance (MR) imaging data were obtained from 248 participants of Alzheimer's disease spectrum (from cognitively normal to Alzheimer's disease dementia). Read More

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http://dx.doi.org/10.1007/s12149-020-01445-yDOI Listing

Symmetry determination and nonlinearization of a nonlinear time-fractional partial differential equation.

Authors:
Zhi-Yong Zhang

Proc Math Phys Eng Sci 2020 Jan 29;476(2233):20190564. Epub 2020 Jan 29.

College of Science, Minzu University of China, Beijing 100081, People's Republic of China.

We first show that the infinitesimal generator of Lie symmetry of a time-fractional partial differential equation (PDE) takes a unified and simple form, and then separate the Lie symmetry condition into two distinct parts, where one is a linear time-fractional PDE and the other is an integer-order PDE that dominates the leading position, even completely determining the symmetry for a particular type of time-fractional PDE. Moreover, we show that a linear time-fractional PDE always admits an infinite-dimensional Lie algebra of an infinitesimal generator, just as the case for a linear PDE and a nonlinear time-fractional PDE admits, at most, finite-dimensional Lie algebra. Thus, there exists no invertible mapping that converts a nonlinear time-fractional PDE to a linear one. Read More

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http://dx.doi.org/10.1098/rspa.2019.0564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7016549PMC
January 2020

Extension of the Quantum Universal Exchange Language to precision medicine and drug lead discovery. Preliminary example studies using the mitochondrial genome.

Authors:
Barry Robson

Comput Biol Med 2020 Feb 20;117:103621. Epub 2020 Jan 20.

Ingine Inc., Delaware, USA; The Dirac Foundation, OxfordShire, UK. Electronic address:

The Quantum Universal Exchange Language (Q-UEL) based on Dirac notation and algebra from quantum mechanics, along with its associated data mining and Hyperbolic Dirac Net (HDN) for probabilistic inference, has proven to be a useful architectural principle for knowledge management, analysis and prediction systems in medicine. It has been described in several papers; here is described its extension to clinical genomics and precision medicine. Two use cases are studied: (a) bioinformatics in clinical decision support especially for risk for type 2 diabetes using mitochondrial patient DNA sequences, and (b) bioinformatics and computational biology (conformational) research examples related to drug discovery involving the recently discovered class of mitochondrial derived peptides (MDPs). Read More

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http://dx.doi.org/10.1016/j.compbiomed.2020.103621DOI Listing
February 2020

SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology.

Bioinformatics 2020 May;36(10):3207-3214

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

Motivation: The Gene Ontology (GO) is the unifying biological vocabulary for codifying, managing and sharing biological knowledge. Quality issues in GO, if not addressed, can cause misleading results or missed biological discoveries. Manual identification of potential quality issues in GO is a challenging and arduous task, given its growing size. Read More

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http://dx.doi.org/10.1093/bioinformatics/btaa106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214018PMC

Evaluating Winding Numbers and Counting Complex Roots Through Cauchy Indices in Isabelle/HOL.

J Autom Reason 2020 3;64(2):331-360. Epub 2019 Apr 3.

Computer Laboratory, University of Cambridge, Cambridge, UK.

In complex analysis, the winding number measures the number of times a path (counter-clockwise) winds around a point, while the Cauchy index can approximate how the path winds. We formalise this approximation in the Isabelle theorem prover, and provide a tactic to evaluate winding numbers through Cauchy indices. By further combining this approximation with the argument principle, we are able to make use of remainder sequences to effectively count the number of complex roots of a polynomial within some domains, such as a rectangular box and a half-plane. Read More

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http://dx.doi.org/10.1007/s10817-019-09521-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995451PMC

Quantitative FTA using Monte Carlo analyses in a pharmaceutical plant.

Eur J Pharm Sci 2020 Apr 13;146:105265. Epub 2020 Feb 13.

Departamento de Engenharia Química / Laboratório de Engenharia de Polimerização - EngePol / Escola de Química, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira, 149, Rio de Janeiro 21941-909 RJ, Brasil.

The evaluation of faults in a multipurpose pharmaceutical pilot plant used for production of polymer particles was performed, integrating traditional Fault Tree Analyses (FTA) and Monte Carlo procedures and employing tools of the quality risk management methodology for production of medicines. The plant was divided into four basic processes: (i) receipt and sampling of materials; (ii) treatment of purified water; (iii) reaction; and (iv) lyophilization and purification. For each process, the most critical failure was selected, and the FTA was built. Read More

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http://dx.doi.org/10.1016/j.ejps.2020.105265DOI Listing

Spacetime Structure near Generic Horizons and Soft Hair.

Phys Rev Lett 2020 Jan;124(4):041601

Institute for Theoretical Physics, TU Wien, Wiedner Hauptstrasse 8-10/136, A-1040 Vienna, Austria.

We explore the spacetime structure near nonextremal horizons in any spacetime dimension greater than two and discover a wealth of novel results: (i) Different boundary conditions are specified by a functional of the dynamical variables, describing inequivalent interactions at the horizon with a thermal bath. (ii) The near horizon algebra of a set of boundary conditions, labeled by a parameter s, is given by the semidirect sum of diffeomorphisms at the horizon with "spin-s supertranslations." For s=1 we obtain the first explicit near horizon realization of the Bondi-Metzner-Sachs algebra. Read More

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http://dx.doi.org/10.1103/PhysRevLett.124.041601DOI Listing
January 2020

Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra.

J Comput Chem 2020 May 14;41(12):1209-1227. Epub 2020 Feb 14.

Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico.

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 (http://tomocomd.com/qubils-midas) are reported in this article since the v1. Read More

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http://dx.doi.org/10.1002/jcc.26167DOI Listing